[gmx-users] unusual error in Gromacs

[soumadwip ghosh]

Dear users,
                 I was trying to equilibrate my system containing a ssDNA,
CNT, water and some ions. I observed that it took many steps for the energy
minimization of the system and after 7/8 steps the potential finally
converged < 500 steps in a steepest descent method. Now, with that system I
proceeded to NVT equilibration. Initially, by keeping the dt= 0.002 an
error saying that

'A charged group moved too far between two domain decomposition steps'

Then I decreased the dt to 0.001 and finally to 0.0005 and tried to
equilibrate the system at NVT first for 200 ps and then for 1 ns and 2 ns
respectively. The temp of the system got converged nicely. Now, when I
increased the dt to 0.001 while running mdrun I'm getting this error-

Program mdrun, VERSION 4.5.6
Source code file: ../../include/vec.h, line: 765

Fatal error:
Can not invert matrix, determinant =

Then I went back to the dt = 0.0005 and tried to do mdrun but again this
error occured. It is reported as a bug somewhere on the internet but I dont
know how to fix this. As you can see I am having problems with a simple NVT
equilibration and cant proceed further. Is it really a bug or is it
appearing because my system is not well-equilibrated? Any suggestion would
be of great relief. I am pasting my NVT.mdp file below for your reference.
Any general guidance regarding the handling of the particular error or the
overall equilibration will be greatly appreciated.


title           = OPLS Lysozyme NVT equilibration
define          = -DPOSRES      ; position restrain the protein
; Run parameters
integrator      = md            ; leap-frog integrator
nsteps          = 2000000               ; 2 * 500000 = 1000 ps
dt              = 0.001         ; 2 fs
; Output control
nstxout         = 500           ; save coordinates every 0.2 ps
nstvout         = 500           ; save velocities every 0.2 ps
nstenergy       = 500           ; save energies every 0.2 ps
nstlog          = 500           ; update log file every 0.2 ps
;
freezegrps = 1MY0
freezedim =  Y Y Y
; Bond parameters
continuation    = no            ; first dynamics run
constraint_algorithm = lincs    ; holonomic constraints
constraints     = all-bonds     ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter      = 1             ; accuracy of LINCS
lincs_order     = 4             ; also related to accuracy
; Neighborsearching
ns_type         = grid          ; search neighboring grid cells
nstlist         = 5             ; 10 fs
rlist           = 1.5           ; short-range neighborlist cutoff (in nm)
rcoulomb        = 1.5           ; short-range electrostatic cutoff (in nm)
rvdw            = 1.5           ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype     = PME           ; Particle Mesh Ewald for long-range
electrostatics
pme_order       = 4             ; cubic interpolation
fourierspacing  = 0.16          ; grid spacing for FFT
; Temperature coupling is on
tcoupl          = V-rescale     ; modified Berendsen thermostat
tC-GRPS         = SYSTEM                ; two coupling groups - more
accurate
tau_t           = 0.1           ; time constant, in ps
ref_t           = 300           ; reference temperature, one for each
group, in K
; Pressure coupling is off
pcoupl          = no            ; no pressure coupling in NVT
; Periodic boundary conditions
pbc             = xyz           ; 3-D PBC
; Dispersion correction
DispCorr        = EnerPres      ; account for cut-off vdW scheme
; Velocity generation
gen_vel         = yes           ; assign velocities from Maxwell
distribution
gen_temp        = 300           ; temperature for Maxwell distribution
gen_seed        = -1            ; generate a random seed


I changed the dt as required and this 1MYO is my CNT. Thanks for your time.

Regards,
Soumadwip Ghosh
Research Fellow,
IITB, Mumbai
India.